© S.J. Coles 2006 Institutional Data Repositories for Chemistry Simon Coles School of Chemistry,...
21
© S.J. Coles 2006 Institutional Data Repositories for Chemistry Simon Coles School of Chemistry, University of Southampton, U.K. [email protected]
-
Upload
noah-castillo -
Category
Documents
-
view
217 -
download
1
Transcript of © S.J. Coles 2006 Institutional Data Repositories for Chemistry Simon Coles School of Chemistry,...
© S.J. Coles 2006
Institutional Data Repositories for Chemistry
Simon Coles
School of Chemistry,
University of Southampton, U.K.
© S.J. Coles 2006
Why? Funding Body Viewpoint
© S.J. Coles 2006
Why? Curation in the Laboratory
“Data from experiments conducted as recently as six months ago might be suddenly deemed important, but those researchers may never find those numbers – or if they did might not know what those numbers meant”
“Lost in some research assistant’s computer, the data are often irretrievable or an undecipherable string of digits”
“To vet experiments, correct errors, or find new breakthroughs, scientists desperately need better ways to store and retrieve research data”
“Data from Big Science is … easier to handle, understand and archive. Small Science is horribly heterogeneous and far more vast. In time Small Science will generate 2-3 times more data than Big Science.”
‘Lost in a Sea of Science Data’ S.Carlson, The Chronicle of Higher Education (23/06/2006)
© S.J. Coles 2006
Why?Publishing and the Data Deluge
Cl
Cl
Cl
Cl
Cl
Cl
ClCl Cl
Cl
Cl
ClCl
O
O
O
O
N
N
N
N
N+
O
O
O
N+
O
O
O
30,000,000
1.5,000,000
450,000
© S.J. Coles 2006
Why?Publishing Data and Information Loss
© S.J. Coles 2006
Separating Data from Interpretations Underlying data
(Institutional data repository)
Intellect & Interpretation
(Journal article, report,
etc)
© S.J. Coles 2006
Data capture and curation at the point of generation in the laboratory
The Repository for the Laboratory – R4L
© S.J. Coles 2006
Laboratory IRs and Information Management
© S.J. Coles 2006
The R4L Repository
Deposit
Search / Browse
Create new compound Add experiment data and metadata
© S.J. Coles 2006
Data dissemination and curation by the scientist and host institution
eBank-UK and the eCrystals Repository
© S.J. Coles 2006
The eCrystals Data Archive
http://ecrystals.chem.soton.ac.uk
© S.J. Coles 2006
Metadata Publication
• Using simple Dublin Core • Crystal structure• Title (Systematic IUPAC Name)• Authors• Affiliation• Creation Date
• Additional chemical information through Qualified Dublin Core• Empirical formula• International Chemical Identifier (InChI)• Compound Class & Keywords
• Specifies which ‘datasets’ are present in an entry
• DOI http://dx.doi.org/10.1594/ecrystals.chem.soton.ac.uk/145
• Rights & Citation http://ecrystals.chem.soton.ac.uk/rights.html
• Application Profile http://www.ukoln.ac.uk/projects/ebank-uk/schemas/
© S.J. Coles 2006
Metadata and Data Quality Control Data manipulation toolbox
Associated Metadata
Value added
Format conversion
© S.J. Coles 2006
Laboratory Data Management and Archive
© S.J. Coles 2006
Institutional data repositories and harvesting, aggregation and curation
by data centres and third party services
eBank-UK Phase 3 – The eCrystals Federation
© S.J. Coles 2006
Aggregator services
Institutional data repositoriesValidation
Deposit
Publication
Validation
Data analysis, transformation, mining, modelling
Search, harvest
Presentation services / portals
Data discovery, linking, citation
Laboratory repositoryDeposit
The eCrystals ‘Global Federation’ Model
Publishers: peer-review journals, conference proceedings, etc
Curation
Preservation
Subject Repository
Institution Library & Information Services
© S.J. Coles 2006
Exploring the heterogeneous landscape of data repositories
• Different software platforms
• Different administrative domains
• Different Institutional structure
• Institutional vs Subject repositories
• Data Repository Interoperability ORE
© S.J. Coles 2006
Preservation and curation
by data centres & Institutions
G bytesM bytes
k bytes
Institution Library & Information Services
© S.J. Coles 2006
Harvesting, aggregation, value
addition and curation by data centres
© S.J. Coles 2006
The relationship with (conventional?) publication protocols and procedures
• Discipline-based publication
• Domain-based publication
• Open Access publication
© S.J. Coles 2006
Aggregation, linking and information provision by third party services
• Indexing and aggregating with other datasets
• Aggregating and linking between datasets and articles
• Integration into information portals
